miR-Intess: classification

other hairpins

block1345 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.521	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	19	13	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------UUGGUUG----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------GTTGGTTGGGACTGCTTTTG----------------------------------------------------------------------	20	1
cbriggsae	tcgtaattcgttcgaaaatGTTGGTTGGGACTGCTTTTGaaatataaatattataaaaattagaaacaatcaagagagagggagaatcatagtttgggtggggaaaaga
	*************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------	NM_214211
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_172925
	-----------------------------------------------------------------------------------------------------------------------	NM_001011629
	-----------------------------------------------------------------------------------------------------------------------	NM_001035248
	-----------------------------------------------------------------------------------------------------------------------	NM_057428
	-----------------------------------------------------------------------------------------------------------------------	NM_001062274
	-----------------------------------------------------------------------------------------------------------------------	NM_001005123
	-----------------------------------------------------------------------------------------------------------------------	NM_001091987
	-----------------------------------------------------------------------------------------------------------------------	NM_001069872
	-----------------------------------------------------------------------------------------------------------------------	NM_001069872
	-----------------------------------------------------------------------------------------------------------------------	NM_205075
	-----------------------------------------------------------------------------------------------------------------------	NM_001037113
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_133195
	-----------------------------------------------------------------------------------------------------------------------	NM_001022613
	-----------------------------------------------------------------------------------------------------------------------	NM_001019821
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_007496
	-----------------------------------------------------------------------------------------------------------------------	NM_003333
	-----------------------------------------------------------------------------------------------------------------------	NM_003333
	-----------------------------------------------------------------------------------------------------------------------	NM_001033930
	-----------------------------------------------------------------------------------------------------------------------	NM_001076363
	-----------------------------------------------------------------------------------------------------------------------	NM_001124194
	-----------------------------------------------------------------------------------------------------------------------	NM_001126212
	-----------------------------------------------------------------------------------------------------------------------	NM_001009286
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_065840
	-----------------------------------------------------------------------------------------------------------------------	NM_080331
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_024149
cbriggsae	......((((..((((.....(((((....((.(((((((.........(((.....))).........)))))))...))...)))))...))))..)))).......	0.590 -14.77

cbriggsae

chromosome:chrIII:2935496:2935604:-1

Opposite_strand|Intronic_coding|NM_214211|UBA52 ## Same_strand|Intronic_non-coding|NM_172925|Klhl31 ## Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_065840|SR-famA ## {Repeats: AT_rich 1 23 -1 class=Low_complexity}

block1725 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.347	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	6	23	5arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	-------AGGAAAG---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------GAGGAAAGCGTTGTTTTGAGT--------------------------------------------------------------------------------------	21	1
cbriggsae	tgatgcGAGGAAAGCGTTGTTTTGAGTcaattgctgatgtggtggacgagggaagtgttggatttgcaccactccagccggtgtagggaacaattgtggagctcctgggatca
	*****************************************************************************************************************
	---------------------------------------------------------------------------------------------------------------------------	NM_111381
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_139424
	---------------------------------------------------------------------------------------------------------------------------	NM_180185
	---------------------------------------------------------------------------------------------------------------------------	NM_023879
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001115091
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001085641
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_080500
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_080504
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_169728
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_169729
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_169730
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_206497
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_131119
	<<<<<----------------------------------------------------------------------------------------------------------------------	NM_001027525
	<<<<<----------------------------------------------------------------------------------------------------------------------	NM_001027524
cbriggsae	.(((...((((..((((((((((....((...((((..((((((..((((............))))))))))..))))...))...)))))))).)).....))))...))).	0.910 -26.70

cbriggsae

chromosome:chrIII:7152352:7152464:1

Opposite_strand|Intronic_non-coding|NM_111381|AT3G05090 ## Same_strand|Intronic_coding|NM_139424|CG11814 ## Opposite_strand|Intronic_coding|NM_023879|Rpgrip1 ## {Repeats: no}

block1925 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.974	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	6	11	5arm	2	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	-------UUUCGAA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------CTTTCGAAGTTCAACTGGCTCC------------------------------------------------------------------	22	1
cbriggsae	gccagcCTTTCGAAGTTCAACTGGCTCCgcagttttgggacgtgctggaatctctgatcggaacaatgctctgttgacaagtggaactgatgct
	**********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_182297
	--------------------------------------------------------------------------------------------------------	NM_005650
	--------------------------------------------------------------------------------------------------------	NM_181492
cbriggsae	(((((..(((((....(((((.((((((((((.(((.((.....)).)))...)))..)))).....)))..)))))....))))))))..)).	0.450 -19.60

cbriggsae

chromosome:chrIV:1231607:1231700:-1

Same_strand|Intronic_non-coding|NM_182297|B0546.4 ## Opposite_strand|Intronic_non-coding|NM_005650|TCF20 ## {Repeats: no}

block2042 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.771	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	13	8	5arm	1	nd	0.30	5	1	1	na	na

		reads	miRBase family seed
seed	--------------UGUCCAG-------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------TTGTCCAGTCATAGTTATAC-------------------------------------------------------------------------	20	1
cbriggsae	gtttcggtgttagTTGTCCAGTCATAGTTATACacaaaataaataaaaaaaacggtaaacacataatattttcgaattgtgactttcttttcggtcagtactggaa
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001105717
	--------------------------------------------------------------------------------------------------------------------	NM_198022
cbriggsae	.((((((((....(((.((((((((((((......((((((.........................))))))..))))))))))........)).)))))))))))	0.830 -14.41

cbriggsae

chromosome:chrIV:3154039:3154144:-1

Same_strand|Intronic_non-coding|NM_001105717|Dpysl2 ## Opposite_strand|Intronic_non-coding|NM_198022|Tnrc6c ## {Repeats: no}

block2050 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.090	no	no	0.48/0.48	21/21/1.00	0.0	0.0	2	0	1	0	6	21	3arm	1	nd	0.19	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------GGCAGUA-------------------	2	novel
		len	cloning frequencies
			AF16
	-------------------------------------------------------------------------TGGCAGTAGTGTTGGGAGTAT------	21	2
cbriggsae	gtaaaaagtttacatttcaaaaaattgctatttcaaaatggttatcaatttgtggttcagtttttgaaagtgtTGGCAGTAGTGTTGGGAGTATttttgc
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001105717
	--------------------------------------------------------------------------------------------------------------	NM_198022
	--------------------------------------------------------------------------------------------------------------	NM_020066
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001047490
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001047489
cbriggsae	(((((((...(((.((((((...(((((((((((((((.....((((.....)))).....))))))))....)))))))....))))))))))))))))	0.980 -20.20

cbriggsae

chromosome:chrIV:3283296:3283395:-1

Same_strand|Intronic_non-coding|NM_001105717|Dpysl2 ## Opposite_strand|Intronic_non-coding|NM_198022|Tnrc6c ## Opposite_strand|Intronic_coding|NM_020066|FMN2 ## Same_strand|Intronic_coding|NM_001047490|nhr-97 ## {Repeats: no}

block2235 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.974	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	6	11	5arm	2	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	-------UUUCGAA--------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	------CTTTCGAAGTTCAACTGGCTCC------------------------------------------------------------------	22	1
cbriggsae	gccagcCTTTCGAAGTTCAACTGGCTCCgcagttttgggacgtgctggaatctctgatcggaacaatgctctgttgacaagtggaactgatgct
	**********************************************************************************************
	--------------------------------------------------------------------------------------------------------	NM_001014737
	--------------------------------------------------------------------------------------------------------	NM_001014738
	--------------------------------------------------------------------------------------------------------	NM_001014739
	--------------------------------------------------------------------------------------------------------	NM_080349
	--------------------------------------------------------------------------------------------------------	NM_167375
	--------------------------------------------------------------------------------------------------------	NM_167376
	--------------------------------------------------------------------------------------------------------	NM_014660
	--------------------------------------------------------------------------------------------------------	NM_001076831
	--------------------------------------------------------------------------------------------------------	NM_001090075
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001030400
	--------------------------------------------------------------------------------------------------------	NM_001047939
	--------------------------------------------------------------------------------------------------------	NM_009930
	--------------------------------------------------------------------------------------------------------	NM_000092
	--------------------------------------------------------------------------------------------------------	NM_000088
	--------------------------------------------------------------------------------------------------------	NM_001007157
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001091797
	--------------------------------------------------------------------------------------------------------	NM_179831
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_214491
cbriggsae	(((((..(((((....(((((.((((((((((.(((.((.....)).)))...)))..)))).....)))..)))))....))))))))..)).	0.450 -19.60

cbriggsae

chromosome:chrIV:10898037:10898130:-1

Opposite_strand|Intronic_coding|NM_001014737|up ## Same_strand|Intronic_non-coding|NM_001030400|cnot4 ## Same_strand|Intronic_coding|NM_001091797|kif15-b ## {Repeats: no}

block3337 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.554	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	11	24	5arm	3	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------UGUCGCG---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------TTGTCGCGGTACTGGAAGCC---------------------------------------------------------------------------------------	20	1
cbriggsae	tcaaaaggacaTTGTCGCGGTACTGGAAGCCatcaaagtaggatatcactcggggaaagcactttgagcactgatgagaaagatggtcctctccgtttggacaccggtcaagcatgaa
	**********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_061817
cbriggsae	(((....(((..((((((((....((..((((((.........((((((((((((......)))))))...))))).....))))))))...))))...))))...))).....))).	0.650 -28.34

cbriggsae

chromosome:chrUn:6791533:6791650:-1

Same_strand|Intronic_non-coding|NM_061817|cct-3 ## {Repeats: no}

block3603 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.554	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	11	24	5arm	3	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------UGUCGCG---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------TTGTCGCGGTACTGGAAGCC---------------------------------------------------------------------------------------	20	1
cbriggsae	tcaaaaggacaTTGTCGCGGTACTGGAAGCCatcaaagtaggatatcactcggggaaagcactttgagcactgatgagaaagatggtcctctccgtttggacaccggtcaagcatgaa
	**********************************************************************************************************************
cbriggsae	(((....(((..((((((((....((..((((((.........((((((((((((......)))))))...))))).....))))))))...))))...))))...))).....))).	0.650 -28.34

cbriggsae

chromosome:chrUn:6807740:6807857:1

{Repeats: no}

block3623 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.016	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	14	0	3arm	1	nd	0.21	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------CUAUACU------------------------------	1	novel
		len	cloning frequencies
			AF16
	-----------------------------------------------------------TCTATACTTTCTACCGGTCCAAGT--------------	24	1
cbriggsae	ggatgacctaaattttcgaaattttgataacaagaaagtaataatagaacattctcaccTCTATACTTTCTACCGGTCCAAGTtttgatgatcacca
	*************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001847
	-----------------------------------------------------------------------------------------------------------	NM_001028815
	-----------------------------------------------------------------------------------------------------------	NM_170227
	-----------------------------------------------------------------------------------------------------------	NM_001012945
	-----------------------------------------------------------------------------------------------------------	NM_001114052
	-----------------------------------------------------------------------------------------------------------	NM_001130158
	-----------------------------------------------------------------------------------------------------------	NM_012223
cbriggsae	((.(((......((.(((((((((.(((....((((((((....((((...........))))))))))))....))).))))))))).))))))).	0.900 -19.00

cbriggsae

chromosome:chrV:577081:577177:-1

Same_strand|Intronic_coding|NM_001847|COL4A6 ## Opposite_strand|Intronic_coding|NM_001028815|F56H9.6 ## Opposite_strand|Intronic_non-coding|NM_001012945|DNAJA1 ## {Repeats: no}

block3774 [novel_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.250	no	no	0.30/0.30	23/23/1.00	0.0	0.0	1	0	1	0	11	3	3arm	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------UAUGCUU--------------------------	1	novel
		len	cloning frequencies
			AF16
	-------------------------------------------GTATGCTTCATTATCTTATTCAC-----------	23	1
cbriggsae	tgaagttgaccaataagatacgaaatgaaatggataaaaatatGTATGCTTCATTATCTTATTCACaagaattttat
	*****************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001011629
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082367
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	NM_001082235
	---------------------------------------------------------------------------------------	NM_005334
cbriggsae	(((((((....(((((((((....((((((((.(((....))).)))..))))))))))))))......))))))).	1.000 -10.10

cbriggsae

chromosome:chrV:9348163:9348239:-1

Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_001082367|ROCK1 ## Opposite_strand|Intronic_non-coding|NM_005334|HCFC1 ## {Repeats: no}

Page 34

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Page 70

miR-Intess™

block1345 [novel_bulgeHIGH]

block1725 [novel_bulgeHIGH]

block1925 [novel_bulgeHIGH]

block2042 [novel_bulgeHIGH]

block2050 [novel_bulgeHIGH]

block2235 [novel_bulgeHIGH]

block3337 [novel_bulgeHIGH]

block3603 [novel_bulgeHIGH]

block3623 [novel_bulgeHIGH]

block3774 [novel_bulgeHIGH]